Yes, many addons allow you to blacklist spells, and that's great. I can blacklist a ton of spells that don't have actual cooldowns. But it doesn't solve the problem. Abilities I do want to know the cooldown of still have a rune cost and improperly appear as on cooldown when the runes are used up.
TellMeWhen: Yes, I can make it only show what I want, but what I want shows up at improper times because of rune cooldowns. Not to mention I don't like the setup, from what I can find it has no way of telling me how long a cooldown has left.
The one addon I have found that KIND OF works how I want it to is
CooldownWatch. It doesn't seem to show abilities when their runes are used up, it probably works different from most cooldown mods. However, whenever you actually use an ability, then use all it's runes, it freaks out and makes giant bars across the screen. Not to mention it has various bugs, can't display pet cooldowns as-is, and is tedious to setup, with the end result not being very effective as an actual cooldown display (I've tried it before, I just don't like it).
All in all, it's extremely frustrating, and I hope Blizzard changes it, or someone comes up with a good solution via mods.
On the subject of actual rune displays, I think people should be taking another look at OOC alpha fading if you plan to do any PvP or are even on a PvP server. Especially if you're fighting a class like a rogue that tries to get out of combat, it isn't a good idea. I can understand not wanting it in your face around Dalaran, but there are times where rune usage is crucial outside of combat.